Dear Swastick,If your question concerns visualizing a deformed system (Nanobubbles in graphene for example) you can do that as follow:
1) Define a new graphene lattice (use: kwant.lattice.general) and introduce the z -component in the vectors and unit cell.
2) Use the option : pos_transform in kwant.plotter.plot to show the buckling.
kwant.plotter.plot(sys, num_lead_cells=2, unit='nn', site_symbol=None, pos_transform=None)
pos_transform: function or NoneTransformation to be applied to the site position.
A result of such use can be seen in this paper [1]
If you want to find how to study quantum transport in deformed systems you can proceed the following way (example of graphene):
1) Keep your system in 2D and not deformed (this will save your memory needs and speed up the calculation)
2) Modify the hopping of the system as induced by the deformation. Example:
# deformation shape
def z(x,y):
a=0.3
return exp(-a*(x**2+y**2))
def hop(site1,site2)
beta=3.37
x1,y1=site1.pos
x2,y2=site2.pos
d0=sqrt((x1-x2)**2+(y1-y2)**2) #distance between connected sites without deformation
d=sqrt((x1-x2)**2+(y1-y2)**2+ (z(x1,y1)-z(x2,y2))**2) # distance after deformation
t=t0* exp(- beta*(d/d0)**2-1) # the change in the hopping due to the deformation
return t
I hope this helps,
Adel
[1] Phys. Rev. B 105, 075425 (2022)